51 lines
1.9 KiB
Python
51 lines
1.9 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
|
|
# Spack Project Developers. See the top-level COPYRIGHT file for details.
|
|
#
|
|
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
|
|
|
|
from spack import *
|
|
|
|
|
|
class Abyss(AutotoolsPackage):
|
|
"""ABySS is a de novo, parallel, paired-end sequence assembler
|
|
that is designed for short reads. The single-processor version
|
|
is useful for assembling genomes up to 100 Mbases in size."""
|
|
|
|
homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
|
|
url = "https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz"
|
|
|
|
version('2.1.4', sha256='2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc')
|
|
version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
|
|
version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c')
|
|
|
|
variant('maxk', values=int, default=0,
|
|
description='''set the maximum k-mer length.
|
|
This value must be a multiple of 32''')
|
|
|
|
depends_on('autoconf', type='build')
|
|
depends_on('automake', type='build')
|
|
depends_on('bwa', type='run')
|
|
|
|
depends_on('mpi')
|
|
depends_on('boost@:1.50.0,1.53.0:', when='@2.0.2:')
|
|
depends_on('boost@:1.50.0,1.53.0:1.59.0', when='@:1.5.2')
|
|
depends_on('sparsehash')
|
|
depends_on('sqlite')
|
|
depends_on('libtool')
|
|
|
|
conflicts('^intel-mpi')
|
|
conflicts('^intel-parallel-studio+mpi')
|
|
conflicts('^mvapich2')
|
|
conflicts('^spectrum-mpi')
|
|
|
|
def configure_args(self):
|
|
maxk = int(self.spec.variants['maxk'].value)
|
|
args = ['--with-boost=%s' % self.spec['boost'].prefix,
|
|
'--with-sqlite=%s' % self.spec['sqlite'].prefix,
|
|
'--with-mpi=%s' % self.spec['mpi'].prefix]
|
|
if maxk:
|
|
args.append('--enable-maxk=%s' % maxk)
|
|
if self.spec['mpi'].name == 'mpich':
|
|
args.append('--enable-mpich')
|
|
return args
|